Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races

Population genomics and molecular epidemiology of wheat powdery mildew in Europe

Agricultural diseases are a major threat to sustainable food production. Yet, for many pathogens we know exceptionally little about their epidemiological and population dynamics, and this knowledge gap is slowing the development of efficient control strategies. Here we study the population genomics and molecular epidemiology of wheat powdery mildew, a disease caused by the biotrophic fungus Blumeria graminis forma specialis tritici (Bgt). We sampled Bgt across two consecutive years, 2022 and 2023, and compiled a genomic dataset of 415 Bgt isolates from 22 countries in Europe and surrounding regions. We identified a single epidemic unit in the north of Europe, consisting of a highly homogeneous population. Conversely, the south of Europe hosts smaller local populations which are less interconnected. In addition, we show that the population structure can be largely predicted by the prevalent wind patterns. We identified several loci that were under selection in the recent past, including fungicide targets and avirulence genes. Some of these loci are common between populations, while others are not, suggesting different local selective pressures. We reconstructed the evolutionary history of one of these loci, AvrPm17, coding for an effector recognized by the wheat receptor Pm17. We found evidence for a soft sweep on standing genetic variation. Multiple AvrPm17 haplotypes, which can partially escape recognition by Pm17, spread rapidly throughout the continent upon its introduction in the early 2000s. We also identified a new virulent variant, which emerged more recently and can evade Pm17 resistance altogether. Overall, we highlight the potential of genomic surveillance in resolving the evolutionary and epidemiological dynamics of agricultural pathogens, as well as in guiding control strategies.

Opportunities and challenges of local ancestry in genetic association analyses

Recently, admixed populations make up an increasing percentage of the US and global populations, and the admixture is not uniform over space or time or across genomes. Therefore, it becomes indispensable to evaluate local ancestry in addition to global ancestry to improve genetic epidemiological studies. Recent advances in representing human genome diversity, coupled with large-scale whole-genome sequencing initiatives and improved tools for local ancestry inference, have enabled studies to demonstrate that incorporating local ancestry information enhances both genetic association analyses and polygenic risk predictions. Along with the opportunities that local ancestry provides, there exist challenges preventing its full usage in genetic analyses. In this review, we first summarize methods for local ancestry inference and illustrate how local ancestry can be utilized in various analyses, including admixture mapping, association testing, and polygenic risk score construction. In addition, we discuss current challenges in research involving local ancestry, both in terms of the inference itself and its role in genetic association studies. We further pinpoint some future study directions and methodology development opportunities to help more effectively incorporate local ancestry in genetic analyses. It is worth the effort to pursue those future directions and address these analytical challenges because the appropriate use of local ancestry estimates could help mitigate inequality in genomic medicine and improve our understanding of health and disease outcomes.

A portable, nanopore-based genotyping platform for near real-time detection of Puccinia graminis f. sp. tritici lineages and fungicide sensitivity

BACKGROUND

Fungal plant disease outbreaks are increasing in both scale and frequency, posing severe threats to agroecosystem stability, native biodiversity and food security. Among these, the notorious wheat stem rust fungus, Puccinia graminis f.sp. tritici (Pgt), has threatened wheat production since the earliest days of agriculture. New Pgt strains continue to emerge and quickly spread over vast distances through the airborne dispersal of asexual urediniospores, triggering extensive disease outbreaks as these exotic Pgt strains often overcome resistance in dominant crop varieties of newly affected regions. This highlights the urgent need for a point-of-care, real-time Pgt genotyping platform to facilitate early detection of emerging Pgt strains.

RESULTS

In this study, we developed a simple amplicon-based re-sequencing platform for rapid genotyping of Pgt isolates. This system is built around a core set of 276 Pgt genes that we found are highly polymorphic between Pgt isolates and showed that the sequence of these genes alone could be used to accurately type Pgt strains to particular lineages. We also developed a simplistic DNA preparation method and an automated bioinformatic pipeline, to enable these Pgt gene markers to be sequenced and analysed rapidly using the MinION nanopore sequencing device. This approach successfully enabled the typing of Pgt strains within approximately 48 h of collecting Pgt-infected wheat samples, even in resource-limited locations in Kenya and Ethiopia. In addition, we incorporated monitoring capabilities for sequence variations in Pgt genes that encode targets of the azole and succinate dehydrogenase inhibitor fungicides, enabling real-time tracking of potential shifts in fungicide sensitivity.

CONCLUSION

The newly developed Pgt Mobile And Real-time, PLant disEase (MARPLE) diagnostics platform we established, now allows precise typing of individual Pgt strains while simultaneously tracking changes in fungicide sensitivity, providing an early warning system for potential indicators of changes in the Pgt population and emerging fungicide resistance. Further integration of this Pgt MARPLE diagnostics platform into national surveillance programmes will support more informed management decisions and timely responses to Pgt disease outbreaks, helping reduce the devastating crop losses currently caused by this 'cereal killer'.

Genomics Research on the Road of Studying Biology and Virulence of Cereal Rust Fungi

Rust fungi are highly destructive pathogens that pose a significant threat to crop production worldwide, especially cereals. Obligate biotrophy and, in many cases, complex life cycles make rust fungi particularly challenging to study. However, recent rapid advances in sequencing technologies and genomic analysis tools have revolutionised rust fungal research. It is anticipated that the increasing availability and ongoing substantial improvements in genome assemblies will propel the field of rust biology into the post-genomic era, instigating a cascade of research endeavours encompassing multi-omics and gene discoveries. This is especially the case for many cereal rust pathogens, for which continental-scale studies of virulence have been conducted over many years and historical collections of viable isolates have been sequenced and assembled. Genomic analysis plays a crucial role in uncovering the underlying causes of the high variability of virulence and the complexity of population dynamics in rust fungi. Here, we provide an overview of progress in rust genomics, discuss the strategies employed in genomic analysis, and elucidate the strides that will drive cereal rust biology into the post-genomic era.

From Lesions to Lessons: Two Decades of Filamentous Plant Pathogen Genomics

Many filamentous microorganisms, such as fungi and oomycetes, have evolved the ability to colonize plants and cause devastating crop diseases. Coevolutionary conflicts with their hosts have shaped the genomes of these plant pathogens. Over the past 20 years, genomics and genomics-enabled technologies have revealed remarkable diversity in genome size, architecture, and gene regulatory mechanisms. Technical and conceptual advances continue to provide novel insights into evolutionary dynamics, diversification of distinct genomic compartments, and facilitated molecular disease diagnostics. In this review, we discuss how genomics has advanced our understanding of genome organization and plant-pathogen coevolution and provide a perspective on future developments in the field. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Beyond Asexual: Genomics-Driven Progress in Unveiling Sexual Reproduction in Cereal Rust Fungi

Recent advances in genomics technologies have revolutionized our understanding of cereal rust fungi, providing unprecedented insights into the complexities of their sexual life cycle. Genomic approaches, including long-read sequencing, genome assembly, and haplotype phasing technologies, have revealed critical insights into mating systems, genetic diversity, virulence evolution, and host adaptation. Population genomics studies have uncovered diverse reproductive strategies across different cereal rust species and geographic regions, highlighting the interplay between sexual recombination and asexual reproduction. Transcriptomics have begun to unravel the gene expression networks driving sexual reproduction, and complementary omics approaches such as proteomics and metabolomics offer potential insights into the underlying molecular processes. Despite this progress, many aspects of cereal rust sexual reproduction remain elusive. Integrating multiple omics approaches with advanced cell biology techniques can help address these knowledge gaps, particularly in understanding sexual reproduction and its role in pathogen evolution. This comprehensive approach will be crucial for developing more targeted and resilient crop protection strategies, ultimately contributing to global food security. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

From Natural Hosts to Agricultural Threats: The Evolutionary Journey of Phytopathogenic Fungi

Since the domestication of plants, pathogenic fungi have consistently threatened crop production, evolving genetically to develop increased virulence under various selection pressures. Understanding their evolutionary trends is crucial for predicting and designing control measures against future disease outbreaks. This paper reviews the evolution of fungal pathogens from natural habitats to agricultural settings, focusing on eight significant phytopathogens: Pyricularia oryzae, Botrytis cinerea, Puccinia spp., Fusarium graminearum, F. oxysporum, Blumeria graminis, Zymoseptoria tritici, and Colletotrichum spp. Also, we explore the mechanism used to understand evolutionary trends in these fungi. The studied pathogens have evolved in agroecosystems through either (1) introduction from elsewhere; or (2) local origins involving co-evolution with host plants, host shifts, or genetic variations within existing strains. Genetic variation, generated via sexual recombination and various asexual mechanisms, often drives pathogen evolution. While sexual recombination is rare and mainly occurs at the center of origin of the pathogen, asexual mechanisms such as mutations, parasexual recombination, horizontal gene or chromosome transfer, and chromosomal structural variations are predominant. Farming practices like mono-cropping resistant cultivars and prolonged use of fungicides with the same mode of action can drive the emergence of new pathotypes. Furthermore, host range does not necessarily impact pathogen adaptation and evolution. Although halting pathogen evolution is impractical, its pace can be slowed by managing selective pressures, optimizing farming practices, and enforcing quarantine regulations. The study of pathogen evolution has been transformed by advancements in molecular biology, genomics, and bioinformatics, utilizing methods like next-generation sequencing, comparative genomics, transcriptomics and population genomics. However, continuous research remains essential to monitor how pathogens evolve over time and to develop proactive strategies that mitigate their impact on agriculture.

Promises and challenges of crop translational genomics

Crop translational genomics applies breeding techniques based on genomic datasets to improve crops. Technological breakthroughs in the past ten years have made it possible to sequence the genomes of increasing numbers of crop varieties and have assisted in the genetic dissection of crop performance. However, translating research findings to breeding applications remains challenging. Here we review recent progress and future prospects for crop translational genomics in bringing results from the laboratory to the field. Genetic mapping, genomic selection and sequence-assisted characterization and deployment of plant genetic resources utilize rapid genotyping of large populations. These approaches have all had an impact on breeding for qualitative traits, where single genes with large phenotypic effects exert their influence. Characterization of the complex genetic architectures that underlie quantitative traits such as yield and flowering time, especially in newly domesticated crops, will require further basic research, including research into regulation and interactions of genes and the integration of genomic approaches and high-throughput phenotyping, before targeted interventions can be designed. Future priorities for translation include supporting genomics-assisted breeding in low-income countries and adaptation of crops to changing environments.

Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement

Aegilops umbellulata serve as an important reservoir for novel biotic and abiotic stress tolerance for wheat improvement. However, chromosomal rearrangements and evolutionary trajectory of this species remain to be elucidated. Here, we present a comprehensive investigation into Ae. umbellulata genome by generating a high-quality near telomere-to-telomere genome assembly of PI 554389 and resequencing 20 additional Ae. umbellulata genomes representing diverse geographical and phenotypic variations. Our analysis unveils complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes, delineating a distinct evolutionary trajectory of Ae. umbellulata from wheat and its relatives. Furthermore, our data rectified the erroneous naming of chromosomes 4U and 6U in the past and highlighted multiple major evolutionary events that led to the present-day U-genome. Resequencing of diverse Ae. umbellulata accessions revealed high genetic diversity within the species, partitioning into three distinct evolutionary sub-populations and supported by extensive phenotypic variability in resistance against several races/pathotypes of five major wheat diseases. Disease evaluations indicated the presence of several novel resistance genes in the resequenced lines for future studies. Resequencing also resulted in the identification of six new haplotypes for Lr9, the first resistance gene cloned from Ae. umbellulata. The extensive genomic and phenotypic resources presented in this study will expedite the future genetic exploration of Ae. umbellulata, facilitating efforts aimed at enhancing resiliency and productivity in wheat.

Resurgence of wheat stem rust infections in western Europe: causes and how to curtail them

Ten years ago, (black) stem rust - the most damaging of wheat (Triticum aestivum) rusts - re-emerged in western Europe. Disease incidences have since increased in scale and frequency. Here, we investigated the likely underlying causes and used those to propose urgently needed mitigating actions. We report that the first large-scale UK outbreak of the wheat stem rust fungus, Puccinia graminis f. sp. tritici (Pgt), in 2022 may have been caused by timely arrival of airborne urediniospores from southwest Europe. The drive towards later-maturing wheat varieties in the UK may be exacerbating Pgt incidences, which could have disastrous consequences. Indeed, infection assays showed that two UK Pgt isolates from 2022 could infect over 96% of current UK wheat varieties. We determined that the temperature response data in current disease risk simulation models are outdated. Analysis of germination rates for three current UK Pgt isolates showed substantial variation in temperature response functions, suggesting that the accuracy of disease risk simulations would be substantially enhanced by incorporating data from prevailing Pgt isolates. As Pgt incidences continue to accelerate in western Europe, we advocate for urgent action to curtail Pgt losses and help safeguard future wheat production across the region.

Comparative Analysis of the Avirulence Effectors Produced by the Fungal Stem Rust Pathogen of Wheat

Crops are constantly exposed to pathogenic microbes. Rust fungi are examples of these harmful microorganisms, which have a major economic impact on wheat production. To protect themselves from pathogens like rust fungi, plants employ a multilayered immune system that includes immunoreceptors encoded by resistance genes. Significant efforts have led to the isolation of numerous resistance genes against rust fungi in cereals, especially in wheat. However, the evolution of virulence of rust fungi hinders the durability of resistance genes as a strategy for crop protection. Rust fungi, like other biotrophic pathogens, secrete an arsenal of effectors to facilitate infection, and these are the molecules that plant immunoreceptors target for pathogen recognition and mounting defense responses. When recognized, these effector proteins are referred to as avirulence (Avr) effectors. Despite the many predicted effectors in wheat rust fungi, only five Avr genes have been identified, all from wheat stem rust. Knowledge of the Avr genes and their variation in the fungal population will inform deployment of the most appropriate wheat disease-resistance genes for breeding and farming. The review provides an overview of methodologies as well as the validation techniques that have been used to characterize Avr effectors from wheat stem rust. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Race and Virulence Dynamics of Puccinia triticina in China During 2007 to 2021

The challenge of wheat leaf rust on wheat production is a recurring issue. Race identification of Puccinia triticina (Pt) serves as the foundation for preventing and controlling this disease. In a 15-year study, we identified 2,900 isolates of Pt from 20 provinces, cities, or autonomous regions in China during 2007 to 2021 and found 332 virulence phenotypes with 11 predominant phenotypes: PHT (8.3%), THT (5.4%), PHK (4.5%), PHJ (3.7%), THJ (3.6%), SHJ (3.5%), THS (3.3%), FGD (2.9%), THK (2.6%), PHS (2.4%), and PHD (2.0%). The virulence frequency for 40 Lr genes was identified across different years and areas; one major reason for the race dynamics was the attenuation to Lr1 and Lr26, which was more evident in southwest China. Lr9, Lr24, Lr28, Lr38, and Lr42 maintained effectiveness in China, while Lr2c, Lr10, Lr12, Lr14a, Lr14b, Lr22a, Lr33, and Lr36 nearly lost their effectiveness against wheat leaf rust disease. Twelve Lr sites were found to have differences in virulence frequencies with values greater than 20% across various locations; furthermore, the lowest and highest virulence values were observed in north China (Area 1) and northwest China (Area 5), respectively. According to phenotype dynamics, PHT, THT, FGD, THK, and PHS are more likely to persist over time. In addition, much attention should be given toward discovering rising combinations of virulent phenotypes.

Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina

In clonally reproducing dikaryotic rust fungi, non-sexual processes such as somatic nuclear exchange are postulated to play a role in diversity but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. We examined three nuclear-phased genome assemblies of Puccinia triticina, which causes wheat leaf rust disease. We found that the most recently emerged Australian lineage was derived by nuclear exchange between two pre-existing lineages, which originated in Europe and North America. Haplotype-specific phylogenetic analysis reveals that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global P. triticina population representing different combinations of a limited number of haploid genomes. Thus, nuclear exchange seems to be the predominant mechanism generating diversity and the emergence of new strains in this otherwise clonal pathogen. Such genomics-accelerated surveillance of pathogen evolution paves the way for more accurate global disease monitoring.

Genome-Enabled Insights into Downy Mildew Biology and Evolution

Oomycetes that cause downy mildew diseases are highly specialized, obligately biotrophic phytopathogens that can have major impacts on agriculture and natural ecosystems. Deciphering the genome sequence of these organisms provides foundational tools to study and deploy control strategies against downy mildew pathogens (DMPs). The recent telomere-to-telomere genome assembly of the DMP Peronospora effusa revealed high levels of synteny with distantly related DMPs, higher than expected repeat content, and previously undescribed architectures. This provides a road map for generating similar high-quality genome assemblies for other oomycetes. This review discusses biological insights made using this and other assemblies, including ancestral chromosome architecture, modes of sexual and asexual variation, the occurrence of heterokaryosis, candidate gene identification, functional validation, and population dynamics. We also discuss future avenues of research likely to be fruitful in studies of DMPs and highlight resources necessary for advancing our understanding and ability to forecast and control disease outbreaks.

From Gene-for-Gene to Resistosomes: Flor's Enduring Legacy

The gene-for-gene model proposed by H. H. Flor has been one of the fundamental precepts of plant-pathogen interactions that has underpinned decades of research towards our current concepts of plant immunity. The broad validity of this model as an elegant and accurate genetic description of specific recognition events between the products of plant resistance (R) and pathogen avirulence (Avr) genes has been demonstrated many times over in a wide variety of plant disease systems. In recent years detailed molecular and structural analyses have provided a deep understanding of the principles by which plant immune receptors recognize pathogen effectors, including providing molecular descriptions of many of the genetic loci in flax and flax rust characterized by Flor. Recent advances in molecular and structural understanding of immune receptor recognition and activation mechanisms have brought the field to a new level, where rational design of novel receptors through engineering approaches is becoming a realizable goal. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Physiological specialization of Puccinia triticina and genome-wide association mapping provide insights into the genetics of wheat leaf rust resistance in Iran

Leaf rust caused by Puccinia triticina Erikss. (Pt) is the most widely distributed and important wheat disease worldwide. The objective of the present study was to determine the frequency of Iranian Pt races, their virulence to key resistance genes and map quantitative trait loci (QTL) for resistance to different Pt races from 185 globally diverse wheat genotypes using a genome-wide association study (GWAS) approach. The virulence pattern of the 33 Pt isolates from various wheat-growing areas of Iran on 55 wheat differentials showed that the FKTPS and FKTTS were relatively frequent pathotypes among the 18 identified races. The weighted average frequency of virulence on the resistance genes Lrb, Lr3bg, Lr14b, Lr16, Lr24, Lr3ka, Lr11 and Lr20 were high (> 90%). However, low virulence on the resistant genes Lr2a, Lr9, Lr19, Lr25, Lr28 and Lr29 indicates that these genes are still effective against the pathogen population in Iran at present. GWAS on a panel of 185 wheat genotypes against 10 Pt races resulted into 62 significant marker-trait associations (MTAs) belonged to 34 quantitative trait loci (QTL) across 16 chromosomes. Among them, 10 QTLs on chromosomes 1A, 1B, 3B, 3D, 4A, 6D, 7A and 7D were identified as potential novel QTLs, of which four QTLs (QLr.iau-3B-2, QLr.iau-7A-2, QLr.iau-7A-3 and QLr.iau-7D-2) are more interesting, as they are associated with resistance to two or more Pt races. The known and novel QTLs associated with different Pt races found here, can be used in future wheat breeding programs to recombine different loci for durable resistance against leaf rust races.